NM_018217.3:c.1084G>C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_018217.3(EDEM2):c.1084G>C(p.Glu362Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,850 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018217.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EDEM2 | NM_018217.3 | c.1084G>C | p.Glu362Gln | missense_variant | Exon 9 of 11 | ENST00000374492.8 | NP_060687.2 | |
EDEM2 | NM_001145025.2 | c.973G>C | p.Glu325Gln | missense_variant | Exon 8 of 10 | NP_001138497.1 | ||
MMP24-AS1-EDEM2 | NM_001355008.2 | c.961G>C | p.Glu321Gln | missense_variant | Exon 13 of 15 | NP_001341937.1 | ||
EDEM2 | NR_026728.2 | n.1378G>C | non_coding_transcript_exon_variant | Exon 8 of 10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EDEM2 | ENST00000374492.8 | c.1084G>C | p.Glu362Gln | missense_variant | Exon 9 of 11 | 1 | NM_018217.3 | ENSP00000363616.3 | ||
EDEM2 | ENST00000374491.3 | c.973G>C | p.Glu325Gln | missense_variant | Exon 8 of 10 | 1 | ENSP00000363615.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251398Hom.: 1 AF XY: 0.0000147 AC XY: 2AN XY: 135860
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461850Hom.: 1 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727222
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1084G>C (p.E362Q) alteration is located in exon 9 (coding exon 9) of the EDEM2 gene. This alteration results from a G to C substitution at nucleotide position 1084, causing the glutamic acid (E) at amino acid position 362 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at